Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development
Summary: Stage- and lineage-specific gene expression patterns are controlled by a complex interplay between transcription factors, the epigenetic landscape, and the three-dimensional (3D) structure of the DNA. The 3D structure allows for the formation of DNA loops that juxtaposition distal regulator...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-07-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004225011162 |
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| author | Johanna Tingvall-Gustafsson Christina T. Jensen Jonas Ungerbäck Mikael Sigvardsson |
| author_facet | Johanna Tingvall-Gustafsson Christina T. Jensen Jonas Ungerbäck Mikael Sigvardsson |
| author_sort | Johanna Tingvall-Gustafsson |
| collection | DOAJ |
| description | Summary: Stage- and lineage-specific gene expression patterns are controlled by a complex interplay between transcription factors, the epigenetic landscape, and the three-dimensional (3D) structure of the DNA. The 3D structure allows for the formation of DNA loops that juxtaposition distal regulatory elements to the promoters, allowing for tight control of gene expression. Developing a tool to facilitate the exploration of complex gene regulatory networks based on chromosome configuration data in early lymphocytes, we show that lineage-specific transcription factors target regulatory elements annotated to both lineage-specific and broadly expressed genes. Several regulatory elements annotated to lineage-specific genes were also annotated to alternative promoters in a context-dependent manner, revealing a highly complex interplay between promoters and DREs in early lymphocyte development. These data highlight how efficient annotation procedures for linking distal regulatory elements to target genes provide valuable insights into gene regulatory networks. |
| format | Article |
| id | doaj-art-59da59b346254c37b2ed22582057b4d0 |
| institution | Kabale University |
| issn | 2589-0042 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj-art-59da59b346254c37b2ed22582057b4d02025-08-20T03:50:21ZengElsevieriScience2589-00422025-07-0128711285510.1016/j.isci.2025.112855Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte developmentJohanna Tingvall-Gustafsson0Christina T. Jensen1Jonas Ungerbäck2Mikael Sigvardsson3Division of Molecular Hematology, Lund University, Lund, Sweden; Division of Molecular Medicine and Virology, Linköping University, Lab 1 Level 13, 58135 Linköping, SwedenDivision of Molecular Hematology, Lund University, Lund, SwedenDivision of Molecular Hematology, Lund University, Lund, SwedenDivision of Molecular Hematology, Lund University, Lund, Sweden; Division of Molecular Medicine and Virology, Linköping University, Lab 1 Level 13, 58135 Linköping, Sweden; Allen Institute for Immunology, Seattle, WA, USA; Corresponding authorSummary: Stage- and lineage-specific gene expression patterns are controlled by a complex interplay between transcription factors, the epigenetic landscape, and the three-dimensional (3D) structure of the DNA. The 3D structure allows for the formation of DNA loops that juxtaposition distal regulatory elements to the promoters, allowing for tight control of gene expression. Developing a tool to facilitate the exploration of complex gene regulatory networks based on chromosome configuration data in early lymphocytes, we show that lineage-specific transcription factors target regulatory elements annotated to both lineage-specific and broadly expressed genes. Several regulatory elements annotated to lineage-specific genes were also annotated to alternative promoters in a context-dependent manner, revealing a highly complex interplay between promoters and DREs in early lymphocyte development. These data highlight how efficient annotation procedures for linking distal regulatory elements to target genes provide valuable insights into gene regulatory networks.http://www.sciencedirect.com/science/article/pii/S2589004225011162Chromosome organizationMolecular geneticsEpigeneticsComponents of the immune system |
| spellingShingle | Johanna Tingvall-Gustafsson Christina T. Jensen Jonas Ungerbäck Mikael Sigvardsson Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development iScience Chromosome organization Molecular genetics Epigenetics Components of the immune system |
| title | Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development |
| title_full | Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development |
| title_fullStr | Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development |
| title_full_unstemmed | Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development |
| title_short | Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development |
| title_sort | chromatin interaction based annotation of regulatory elements reveals dynamic promoter enhancer interactions in lymphocyte development |
| topic | Chromosome organization Molecular genetics Epigenetics Components of the immune system |
| url | http://www.sciencedirect.com/science/article/pii/S2589004225011162 |
| work_keys_str_mv | AT johannatingvallgustafsson chromatininteractionbasedannotationofregulatoryelementsrevealsdynamicpromoterenhancerinteractionsinlymphocytedevelopment AT christinatjensen chromatininteractionbasedannotationofregulatoryelementsrevealsdynamicpromoterenhancerinteractionsinlymphocytedevelopment AT jonasungerback chromatininteractionbasedannotationofregulatoryelementsrevealsdynamicpromoterenhancerinteractionsinlymphocytedevelopment AT mikaelsigvardsson chromatininteractionbasedannotationofregulatoryelementsrevealsdynamicpromoterenhancerinteractionsinlymphocytedevelopment |